Why did Atticus look like "his stomach hurt" after questioning Mayella during the trial?

I think that there are three possible reasons why Atticus
might feel this way.

First, I think he probably feels bad
for having cross-examined her the way that he has.  I think he feels bad that he had to
ask her the sorts of personal questions he did and he feels bad for having to sort of
bully her, trying to get her to admit the truth.

Second, I
think that he probably feels sorry for her.  If you knew that this girl had a father who
treats her the way Mayella's dad does, how would you
feel?

Finally, I think he may feel that he has lost the
case already.  He may feel that his only hope was to get Mayella to confess the
truth.